Fabrice Senger
@senger.bsky.social
📤 765
📥 409
📝 593
Mechanobiology / Multi-cellular assemblies
Allways a good read, even for the lay
add a skeleton here at some point
2 days ago
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bioRxiv Cell Biology
3 days ago
Optogenetic SH3 nanoclustering of SRC and HCK uncovers the functional specificity of these redundant kinases in macrophages.
https://www.biorxiv.org/content/10.64898/2025.12.27.692121v1
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Nikon Microscope Solutions
5 days ago
💻 Get direct access to 3D CAD models for Nikon microscope components! ✏️Our CAD request page puts detailed, ready-to-use files at your fingertips, so you can design with total precision and speed. 👉 Explore the page and grab your CAD files today: https://bit.ly/3Y4gzOV
#NikonMicroscopy
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Gaëlle Recher
7 days ago
📣 Paper alert A great collaboration with my colleagues from Toulouse 🤝 ANR MOLIERE Big up to Angélique Ala for computing & modelling and Camille Douillet for experimental work
@cnrs.fr
@univbordeaux.bsky.social
@universitetoulouse.bsky.social
@agencerecherche.bsky.social
doi.org/10.1016/j.ac...
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Olivier Pertz
10 days ago
🔬📊 PhD (100%) – Statistics & ML for self-driving microscopy Joint PhD with David Ginsbourger (Stats) & Pertz Lab (Cell Biology). Gaussian Processes, Bayesian design, active learning on live-cell experiments.
ohws.prospective.ch/public/v1/jo...
#PhD
#Statistics
#MachineLearning
#Bayesian
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Uni Bern: PhD Position in Statistics with a focus on Statistical Machine Learning for Self-Driving Microscopy
https://ohws.prospective.ch/public/v1/jobs/a9ae70e1-a720-4a12-bc5a-b7d1b232cb69
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Denis Wirtz
12 days ago
Now that you have gathered you raw data from a cell migration assay, how do you analyze that data? In our review, we describe methods - including AI methods - to track migrating cells and extract as much information as possible. Read our paper here:
www.nature.com/articles/s41...
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Brian Northan
12 days ago
New video: more examples showing deep learning segmentation failure modes—and how to detect them with Napari. I show how Napari’s layer system compares images, ground truth, and results, and how Appose enables comparison across incompatible DL packages.
www.youtube.com/watch?v=c369...
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Using Appose with Pixi and Napari for reproducible deep learning segmentation workflows.
YouTube video by Brian Northan
https://www.youtube.com/watch?v=c369VKAqGY0
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Ricardo Henriques
12 days ago
🚀📰 End-of-year news for
#RxivMaker
=). Now it generates both
#pdf
and
#docx
from
#markdown
. Docx makes it easier to collaborate on a document for non-markdown users, making it simple to loop between docx and
#RxivMaker
to a professional-looking
#preprint
Preprint updated:
arxiv.org/abs/2508.00836
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rdcu.be/eVrRs
What i most like here is the concept of prompt engineering as a basis to use SAM ...
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CellSAM: a foundation model for cell segmentation
Nature Methods - CellSAM uses an object detector, CellFinder, to detect cells and prompt the Segment Anything Model (SAM) to generate segmentations. This universal model achieves human-level...
https://rdcu.be/eVrRs
12 days ago
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Denis Wirtz
13 days ago
We wrote two reviews on cell migration, published today in Nature Methods. They provides practical guidelines how to select a cell-migration assay and how to analyze cell-migration data Review 1:
nature.com/articles/s41...
Review 2:
nature.com/articles/s41...
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James Briscoe
15 days ago
Good to see the peer reviewed version of this published A chemo-optogenetic system for spatiotemporal control of gene expression We use it to: - Reconstruct SHH mediated neural tube patterning in vitro - Measure extracellular half-life of Shh
www.cell.com/developmenta...
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Investigating morphogen and patterning dynamics with optogenetic control of morphogen production
Benzinger et al. develop a chemo-optogenetic system for precise spatiotemporal control of morphogen production in vitro. Using light-controlled Sonic hedgehog expression, they recapitulate neural tube...
https://www.cell.com/developmental-cell/fulltext/S1534-5807(25)00495-2
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Marija Matejčić
15 days ago
I am putting together a collection of video-protocols we (will) use in tissue mechanics research🌀 I hope to help consolidate established methods, but also showcase a few up-and-coming ones in our blooming field. Abstract submission by March 2026! Get in touch✨
#JoVETissueMech
#ReproducibleTissueMech
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Here we go
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15 days ago
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AI-driven Optical Biology Lab
16 days ago
Do you know how far phototoxicity can hinder your experiments?🤔
@mariodelr.bsky.social
and
@gomez-mariscal.bsky.social
have just published their work on
#PhotoFiTT
in
@natcomms.nature.com
where they explain how to quantitatively measure it in live-cell imaging.⚡🧫🔬 Read more at:
shorturl.at/ly9Zn
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Valentin Dunsing-Eichenauer
16 days ago
New paper out! Combining single-objective light-sheet microscopy and time-resolved SPAD array detection, we massively accelerate fluorescence lifetime imaging (FLIM) compared to confocal FLIM, making FLIM applicable to 3D specimen such as organoids and embryos.
www.nature.com/articles/s42...
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bioRxiv Cell Biology
16 days ago
AutoSTED: An automated workflow for STED super-resolution imaging of cell nuclei
https://www.biorxiv.org/content/10.64898/2025.12.11.693650v1
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epithelial mechanics fan club
17 days ago
Cells can sense the geometry of their environment, from tiny subcellular features to whole-tissue patterns. How can we engineer environments to systematically probe these responses? 🧵 I'm
@lhinderling.bsky.social
from
@olivierpertz.bsky.social
lab, let’s do a short tour on microfabrication!
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Zimeng Wu
23 days ago
Pleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (“diss track”) - Dynamic Sample Tracking. It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems. Preprint:
www.biorxiv.org/content/10.6...
[1/6]
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𝙲𝚞𝚛𝚝𝚒𝚜 𝚁𝚞𝚎𝚍𝚎𝚗 (@
[email protected]
)
19 days ago
If you want to learn more about Appose, check out the hands-on Appose workshop from "Halfway to I2K" 2025:
fiji.github.io/i2k-2025-app...
– along with the reference implementation of the demo project at
github.com/ctrueden/uns...
. New releases of python and java flavors coming before year's end.
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Appose Workshop - Slidev
"## Appose: Interprocess Cooperation with Shared Memory\nI2K 2025 Workshop\n\nTeaching participants how to use Appose with Fiji for Python integration\n"
https://fiji.github.io/i2k-2025-appose/
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Qiyun Zhu
20 days ago
The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you.
www.nature.com/articles/s41...
#Bioinformatics
#OpenSource
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Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods
Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis
https://www.nature.com/articles/s41592-025-02981-z
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Wyoming Wormboy
19 days ago
Hot off the press at EMBO Journal. The culmination of several years of work and hopefully useful to people in the field! BIG Shout-out to Review Commons, who handled the submission. It's a sensible and efficient model and all the journals I like (Society and NFP) are already participating. 🙏
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Integrating endogenous TurboID and data-independent acquisition mass spectrometry for in vivo proximity labeling - The EMBO Journal
Proximity labeling has emerged as a powerful approach for identifying protein–protein interaction networks within living systems, particularly those involving weak or transient associations. Here, we ...
https://link.springer.com/article/10.1038/s44318-025-00660-5?utm_source=rct_congratemailt&utm_medium=email&utm_campaign=oa_20251211&utm_content=10.1038%2Fs44318-025-00660-5
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epithelial mechanics fan club
19 days ago
Minin, A., Semerikova, T., Belousova, A.V., Karavashkova, O., Pozdina, V., Tomilina, M., & Zubarev I. (2025). MSLASpheroidStamp: 3d cell spheroids for everyone. Bioprinting, 49, e00416.
#EpithelialMechanics
buff.ly/gwERE1P
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Sally Lowell
20 days ago
Hello, here is a review I wrote about how cells sometimes try to synchronise with surrounding cells so that they can do a good job of building tissues during development. It is called "Keeping up with the neighbours"
link.springer.com/article/10.1...
#DevBio
🧪
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Keeping up with the neighbours: local synchronisation of cell fate decisions during development - EMBO Reports
Even before the advent of multicellular life, unicellular creatures would communicate with their neighbours to coordinate their behaviours. Multicellular organisms have the particular challenge of orc...
https://link.springer.com/article/10.1038/s44319-025-00662-8
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Isn't it that biorixv is on fire ?
20 days ago
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Jean-Yves Tinevez
21 days ago
Yep exactly. SAMJ is based on the preview off a brand new technology called appose that does everything transparently (download etc) TrackMate 9 will be based on that Summoning
@ctrue.bsky.social
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Séamus Holden 🔬🦠🧫
20 days ago
@simonecoppola.bsky.social
has made micromorph, the first native Python application and library for measuring bacterial morphology. It runs interactively in napari or can be easily integrated into automated Python scripts. It integrates deep learning cell segmentation and is easily extended 🔬🦠🧫
add a skeleton here at some point
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Erwin Frey
22 days ago
🧪⚛️ “Turing foams” in the Min system—now seen in experiment. Non-equilibrium protein currents create foam-like interfaces obeying Plateau laws and even splitting like tiny dividing cells. Stunning video from Petra Schwille’s lab; the whole story is here:
www.nature.com/articles/s41...
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www.musee-orsay.fr/fr/agenda/ev...
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Quelques secondes d'éternité · Soirée Architectures vivantes
Projetées à une échelle gigantesque sous forme de vidéo mapping, ces images sont le fruit d’un travail expérimental inédit issues des recherches les plus récentes en biologie cellulaire : une série de...
https://www.musee-orsay.fr/fr/agenda/evenements/quelques-secondes-deternite-soiree-architectures-vivantes
23 days ago
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Guillaume Jacquemet
25 days ago
Latest from the lab "Filopodome proteomics identifies CCT8 as a MYO10 interactor critical for filopodia functions "
www.biorxiv.org/content/10.6...
Work driven by
@anagracanin.bsky.social
A great collaboration with
@ivaskalab.bsky.social
and
@bengoult.bsky.social
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Filopodome proteomics identifies CCT8 as a MYO10 interactor critical for filopodia functions
Cancer cells utilize filopodia to explore, adhere to, and invade their surrounding microenvironment, yet the protein networks that organize these protrusions remain incompletely defined. To uncover th...
https://www.biorxiv.org/content/10.64898/2025.12.03.691809v1
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This is going to be breathtaking
add a skeleton here at some point
26 days ago
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Fabrice Senger
FocalPlane
26 days ago
Meet the Epithelial Mechanics Fan Club
@epimechfc.bsky.social
Nimesh Chahare
@onenimesa.bsky.social
and Julia Eckert
@juliaeckert.bsky.social
introduce us to the Epithelial Mechanics Fan Club. Learn how you can get involved with this community:
focalplane.biologists.com/2025/12/04/e...
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Epithelial Mechanics Fan Club - FocalPlane
Epithelial Mechanics Fan Club - News
https://focalplane.biologists.com/2025/12/04/epithelial-mechanics-fan-club/
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Wallace Marshall
26 days ago
Cells can hunt prey, solve mazes, and learn from past experience. Does this mean they can think, at some level? Find out more at our upcoming session on "Cell Behavior and Cognition" at the ASCB/EMBO
#cellbio2025
meeting, Saturday 1-3 pm rm 115.
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Biophysical Journal
27 days ago
Too fluid, too rigid, no patterning. Garner et al. identify tissue fluidity—how freely cells move within a tissue—as a critical regulator of adhesion-based cell sorting. Read their study to learn how tissues can tune their fluidity to enable patterning.
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Tissue fluidity mediates a trade-off between the speed and accuracy of multicellular patterning by cell sorting
The organization of cells into spatial patterns is a fundamental aspect of multicellularity. One major mechanism underlying tissue patterning is adhesion-based cell sorting, in which a heterogeneous…
https://www.cell.com/biophysj/fulltext/S0006-3495(25)00652-6
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Lab on a Chip
27 days ago
In the latest issue of Lab on a Chip: Reversible and reusable compartmentalized thermoplastic chip for coculture of dorsal root ganglion neurons. Hugo Salmon, Sophie Bernard et al
@hugsalmon.bsky.social
@upcite.bsky.social
pubs.rsc.org/en/content/a...
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Reversible and reusable compartmentalized thermoplastic chip for coculture of dorsal root ganglion neurons
Compartmentalized microfluidic chips play an important role in understanding the cellular mechanisms involved in neurodegenerative disorders. Dorsal root ganglia are a well-established model for model...
https://pubs.rsc.org/en/content/articlelanding/2025/LC/d5lc00666j#!divAbstract
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Michael Way
27 days ago
Are you interested in cytoskeleton and looking for a postdoc position? I will be advertising positions in the new year but happy to chat in person if you are attending ASCB
@ascbiology.bsky.social
in Philadelphia. Just drop me a line.
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Denis Wirtz
28 days ago
We used CODA to generate 3D single-cell immuno maps around pre-cancer lesions of the human pancreas. Highly heterogeneous. Work by Prof. Ashley Kiemen and colleagues. Read more about 3D immuno maps around pre-cancer lesions here:
www.biorxiv.org/content/10.1...
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EMBO
28 days ago
The EMBO Practical Course "Hack your microscope" in Oeiras, PT, 20–25 Apr 2026 aims to innovate, democratize advanced #imaging technologies and shape the future of open-source #microscopy – Apply now! Deadline: 12 Dec
https://meetings.embo.org/event/26-microscope
#imaging
#microscopy
#EMBOmicroscope
#EMBOevents
🧪
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Michael Way
28 days ago
SPIN90 and
#YanCao
strike again! First NPF to only activate a subset of Arp2/3 iso-complexes to regulate lamellipodial actin & protrusion efficiency. Great collaboration with
@romet-jegou-lab.bsky.social
#ManosMavrakis
polarized fluorescence microscopy rocks 🤘💥🎉
www.biorxiv.org/content/10.6...
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SPIN90 modulates the architecture of lamellipodial actin in an ARPC5L dependent fashion.
When stimulated by nucleation-promoting factors such as WAVE, the Arp2/3 complex generates branched actin networks. In contrast, when activated by SPIN90, the Arp2/3 complex generates linear actin fil...
https://www.biorxiv.org/content/10.64898/2025.12.01.691495v1
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Santos lab
29 days ago
So exciting to see this in print! Ever wondered how embryonic cells know what (fate) to become during early development? In particular when they might see different signaling cues? We investigated this! And a lovely cover from Zoe Ruiz and
@oliveringe.bsky.social
!
www.cell.com/developmenta...
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Combinatorial BMP4 and activin direct the choice between alternate routes to endoderm in a stem cell model of human gastrulation
Inge et al. show that human endoderm originates from two converging developmental routes with distinct dynamics and efficiencies yet similar developmental potential. Combinatorial activin and BMP4 sig...
https://www.cell.com/developmental-cell/fulltext/S1534-5807%2825%2900529-5
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youtu.be/8UsYLb3O8fI?...
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Mac DeMarco - Holy
YouTube video by Mac DeMarco
https://youtu.be/8UsYLb3O8fI?si=eeEpvyglRRy6ZGYH
29 days ago
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Teun Huijben
30 days ago
Ultrack on the cover of Nature Methods! Thanks
@alexandredizeux.bsky.social
for helping us with the beautiful cover art! 😍
add a skeleton here at some point
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Jon Humphries
29 days ago
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i surprised myself preaching about data structure after being fed up with labels like : Ctrl , ctrl, CTRL etc
29 days ago
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Fabrice Senger
Benoit Ladoux
29 days ago
Tissue stress measurements — our latest preprint is out:
arxiv.org/abs/2512.00550
(publication coming soon!) Fantastic work by the three musketeers —
@luanger.bsky.social
,
@andreasschoenit.bsky.social
and
@fanny-wodrascka.bsky.social
— in collaboration with P. Marcq!
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Tissue stress measurements with Bayesian Inversion Stress Microscopy
Cells within biological tissue are constantly subjected to dynamic mechanical forces. Measuring the internal stress of tissues has proven crucial for our understanding of the role of mechanical forces...
https://arxiv.org/abs/2512.00550
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Fabrice Senger
Journal of Cell Science
29 days ago
In their Tools and Resources article, Nina Grishchenko, Michael Olson and colleagues present Toogle-Untoogle, a cell segmentation tool with an interactive user verification interface.
journals.biologists.com/jcs/article/...
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Fabrice Senger
Hanjin Liu
about 1 month ago
Our latest work is out in biorxiv! 😊 We show that human spastin, a microtubule severing enzyme, behaves completely differently in presence of free tubulin - it forms tubulin ring stack and promotes de novo microtubule nucleation.
www.biorxiv.org/content/10.1...
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Human spastin functions as an ATPase-independent microtubule nucleator via ring-stack formation
Microtubule severing enzyme spastin plays pivotal roles in cytokinesis and neuronal outgrowth, and its mutations cause hereditary spastic paraplegia (HSP). Here we show that, at physiological tubulin ...
https://www.biorxiv.org/content/10.1101/2025.11.28.691112v1
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Bart Smeets
about 1 month ago
Our paper is out in Nature Communications! We combine two-photon microscopy and active foam modeling to show how cell-scale mechanics control the viscoelasticity and fusion of tissue spheroids, linking single-cell behavior to tissue-level properties. 🔗
www.nature.com/articles/s41...
#ActiveMatter
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Active foam dynamics of tissue spheroid fusion - Nature Communications
Combining microscopy and modeling, the authors reveal that tissue fluidity, driven by active cell motion and interfacial tension, governs how living spheroids merge into larger structures.
https://www.nature.com/articles/s41467-025-65463-y
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Fabrice Senger
about 1 month ago
www.nature.com/articles/s41...
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Measuring cellular force using DNA-based tension probes: from ensemble to single-molecule studies - Nature Protocols
The authors present a protocol for the use of two advanced DNA-based tension probes, the reversible shearing DNA-based tension probe (RSDTP) and ForceChrono probe, which provide powerful tools for stu...
https://www.nature.com/articles/s41596-025-01277-y
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Fabrice Senger
Antoine Zalc
about 1 month ago
Hi everyone, Which compagnie to you recommand to purchase siRNA ?? Thank you for your replies! Don't hesitate to share
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Fabrice Senger
Moe Mahjoub
about 1 month ago
New must-read review article for all lovers of
#centrioles
and
#centrosomes
😍👇
add a skeleton here at some point
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